The Writing on the Wall S:0 Ep:5
by Lina Cross
Summary: The Wraith's plans were foiled again, but at a cost. The residents of Atlantis are suffering from mistrust and paranoia, Cooper more than most. An accident on a simple mission forces her worries elsewhere, however, and Sheppard tries desperately to maintain that all is as it should be.
1. Chapter 1

**Sorry for the hiatus!**

**We return to our team a week or so after the events of "I Can't Look." I thank you all for reading this far, and I hope you continue to read, because I still have more plans. Now let's return to an Atlantis that is suffering from a little bit of PTSD.**

**. . .**

Sheppard bolted upright, coated in sweat and breathing heavily. He unclenched his hands from his sheets, where once he'd thought they were clenched around Cooper's throat. The panic in her eyes, the sickening _joy_ he felt at hurting her...

If he was having nightmares, he couldn't imagine what she must be going through.

As much as he loved being on the Atlantis Expedition, Pegasus was having a negative effect on his mind. All those times, whether he was aware of it or not, that he hurt his friends was a blow to his spirit. It was literally the worst thing he could think of. John Sheppard, so aptly named, for he had become a shepherd of the people. He was doing damage to his own flock. It didn't even matter how it happened, whether something stole his face or entered his brain or manipulated him, it was all the same, in the end. His hands did harm to the people he swore to protect.

He threw off the covers, not caring that it was an hour and a half before his alarm, and began getting dressed. In the week or so since she'd been back, Cooper hadn't spoken much to him. The raging guilt he felt at his actions wasn't much helped by the fact that it wasn't his fault. Ironically, it had been his attempt at saving Lorne that had caused him to try to kill Cooper.

It wasn't just him, and it wasn't just his lieutenant. Most of the city was still recovering from the disaster, and some people that had been best friends beforehand could no longer even look at one another. Rodney had been among the fastest to readjust simply because he hadn't exactly hurt anybody, and it hadn't taken much for Sheppard to get ahold of him. Zelenka was twitchy around the colonel, as were a few of the Marines. Elizabeth was doing her best to get her emotions under control. She'd called Sheppard into her office a day or two after the event was over and just talked with him. He was glad for that, because it offered them both a bit of closure on the subject. Teyla was willing to forgive and forget, but Ronon was having trouble forgiving himself.

Cooper, the only one who did only what she had to, who had no reason to regret her actions, had apologized to the whole team for what she did to them. Maybe it helped her deal with the issue, or maybe she really felt like she owed them an apology. Whatever the case, it only served to make Sheppard feel worse.

Because he was up so early, and because he had no intention of going back to sleep, he decided to go for a run. The constant rhythm of his feet would hammer out the oppressive thoughts in his mind.

Almost to the bridge, he heard footsteps and slowed, looking around the shadows. Ronon.

"Can't sleep either?" Sheppard asked, taking this chance to drink water.

He shook his head. "Can't think straight."

"It's been rough. We'll get it together, it'll be fine."

Ronon looked at him, and Sheppard knew he wasn't fooled. No one could make that kind of promise at this point.

"Let's just keep going," he finally said, abandoning the conversation and going back to running. Ronon followed wordlessly, his heavy feet pounding the metal in a steady rhythm.


	2. Chapter 2

"Cooper?"

She paused, looking to the side. "Evan."

"Lunch?" he said, raising an eyebrow and gesturing towards the mess hall.

She glanced in that direction, then nodded. "Sure."

He smiled, a small gesture. He was never one for large displays of emotion. But as she fell into step beside him, he gave a light touch on her lower back. It was the little things she was fond of.

"Mission today, right?" he asked. "Empty planet with some of those ancient ruins you're so fond of. Right up your alley."

She smiled. "Yeah. We're going to translate stuff. And by 'we' I mean me."

"Why is Dr. Weir sending the alpha team, though?" he asked, grabbing two trays and handing her one. "I mean, that's normally something she hands you over to me for."

Her smile retracted slightly. "I think... maybe Dr. Weir is doing this for reconciliation purposes." Lorne gave her a raised eyebrow, so she elaborated. "Ever since the stunner incident, we haven't... _I_ haven't really been able to be with my team. I think she's worried if our relationship isn't repaired quickly, it might never be."

"And are you okay with that? I know..." He faltered, knowing how she hated the subject. "Look, I know how unsafe you feel around the colonel and Ronon. If you're really uncomfortable with this, I can ask that we switch teams for this one."

"No, Dr. Weir's right," she said, shaking her head as they sat at a table. "I _have_ to move past this. I'm sick of feeling jumpy and tense every time one of them walks into the room. The scars on the surface have all healed; I think it's about time the ones underneath did, too."

He reached over and squeezed her hand lightly. "You'll be fine."

"Hey!"

They both looked up, startled, to see Dr. Kavanagh giving them a dirty look. He approached the table, irritation apparent. "Look, you can try and rise up through the ranks any way you want, but don't do it out in public for everyone to watch. Not only is it wrong, it's also disgusting."

She stared at him blankly. "What?"

"Don't think no one's noticed," he said condescendingly. "You're tired of being a lieutenant, you've done enough to get anyone promoted but you're still stuck here. I can understand, I've got the same problem. But I don't fool around with my superiors to get a raise."

"Fun plan, Kavanagh, but I'm not the lead officer she needs if that's her goal," Lorne said acidly. He looked like he wanted to knock the man out cold, but that would cause a scene Cooper didn't want. Instead, she leveled a surprised glare at the major.

"What? Evan, why didn't you say something? I've been sleeping with the wrong CO this whole time!"

He passed a weary hand over his face. "Are you referring to the sex we most definitely have not been having?"

She frowned. "Oh, come on, give the guy a show."

Kavanagh glared at them, knowing she was demeaning him. "I will be reporting this to Dr. Weir."

She threw her hands up as he walked off. "Be my guest! I guarantee, she already knows!"

Lorne looked around at the people who had started giving them amused glances. "That was a fun conversation to have in the middle of the mess."

She shrugged. "I knew somebody was gonna get a burr up their butt about it sooner or later. Better it was from Kavanagh than someone people actually respect."

He snorted, but chose not to further the issue.

**. . .**

"Ah, finally. A planet that doesn't look like the Pacific Northwest," Rodney said as the team exited the wormhole.

"And this is better?" Ronon asked with a raised eyebrow.

"We're not gonna be here too long, it doesn't matter," Cooper said, looking around at the sandy desert landscape. "There's the dig site. We should get this going."

Sheppard glanced at her, saying nothing and allowing her to lead the way. He thought it might be better if he didn't talk.

"Okay, so basically what happened is the last team was digging around and found this," Rodney said, pointing at a large stone slab with a triangular symbol on it. "They were checking it out when someone got a little overexcited, stepped on the plate, and opened that door in the ground fifteen feet away."

"I've never seen you so excited about someone making a mistake, Dr. McKay," Cooper said with a dry smile.

"Because for once, we got something interesting and not very deadly out of it."

"What is it with the Ancients and triangles?" Sheppard asked, looking down at the stone. "We seem to find them a lot."

"Dunno. We haven't found much of a correlation yet," said the scientist.

"I'm assuming the chamber is safe?" Cooper asked, walking over to the rectangular hole in the ground. There was already a pulley system set up for lowering people into the room below.

"According to Dr. Marco, yes, perfectly safe."

"So then you probably want to go first."

"What?" He looked up from his data pad, raising his eyebrows. "Ha, uh, no, no, no, I mean, you're the linguist, you might as well go first, am I right?"

"_I'll _go first," Sheppard said, taking hold of the cable. No one argued, allowing the colonel to lower himself down. Cooper went next, then Teyla, then Rodney, and Ronon volunteered to stay topside to pull everyone back up and keep watch.

Cooper looked around the chamber. It wasn't very big, maybe a bit larger than the cell she shared with Dr. Weir when taken hostage. Writing covered the walls in varying styles, and there was a stone altar-type table off to one side. There were a few pictures on the walls, too, but without knowing what the writing said, the lieutenant figured she wouldn't understand their meaning.

"Recognize any of it?" Sheppard asked.

"I do," Teyla said unexpectedly, staring at the wall. "Almost..."

Cooper took a closer look, then almost smiled. "That's because it's an Ancient dialect. Sort of, ancient Ancient, I guess."

Sheppard made a face. "That's really old."

"Thank you for your input, Colonel," Rodney said dryly. "Your intellect is of immeasurable value."

"Hang on a second," Cooper said, stepping into a small alcove. "I just found the same symbol on the wall, the one that's outside. Do we know what it means?"

"No," said Rodney, looking over at her. "We thought maybe it could be a sort of signature, like a house number or name on a mailbox."

She reached up curiously, brushing her fingers against the mark, when suddenly her entire body felt jarred from head to toe and she collapsed.


	3. Chapter 3

Sheppard had not actually been looking when Cooper and Rodney were talking. But the moment he heard her cry out, he whipped around. A blue light engulfed Cooper like electricity, her body glowing for a terrifying second. She only screamed once, then crumpled to the floor. Before anyone could move, the doorway to the alcove trembled. In a matter of moments, small rocks falling from the ceiling became large ones until the entire doorway had collapsed, trapping Cooper and sending up a thick cloud of dust.

"Cooper!" Sheppard shouted, but Teyla grabbed his arm.

"Wait! John, the ceiling is not stable!"

"She's under there!"

"Teyla's right, just give it a minute!" Rodney shouted, pushing them both back against the far wall. Dust continued to fall, but as they watched, the rest of the ceiling stayed in-tact.

"What happened?" Ronon called.

"Cooper's down! Contact Atlantis, get a medical team and an extraction unit!" The colonel broke free of his friends and moved to the pile of rubble. With any luck, she was far enough into the alcove that she wasn't being crushed under the weight of all that rock. "Hang on, Cooper, we're gonna get you out of there."

**. . .**

"Clear the way! I need that scanner running soon as you can!" Beckett called, wheeling the gurney into the infirmary. Sheppard and his team weren't far behind, which irked the doctor slightly. They couldn't do much, and they'd only get in the way. Cooper was bad off, with at least a major concussion, and no way of immediately knowing the extent of internal damage. She was cocooned in the wheeled bed, an oxygen mask obscuring most of her face, and the rest coated in dirt. Panic was starting to set in with the team.

"She gonna be okay?"

"I don't know, Colonel, I won't know for a little while longer. Please, step outside."

Sheppard gritted his teeth, then whirled around. "Rodney! What happened!"

"Why do you expect me to know? Look, maybe it wasn't structurally sound from the beginning, we didn't exactly make sure the room was up to code!"

"You saw the blue light! Nobody thought to mention there was electricity in there?"

"We don't even know if that _was_ electricity, we saw it for a second! Dr. Marco swears up and down they scanned that entire chamber and found only the faintest energy readings, which only explains how the door was able to open!"

"Looked like a booby trap to me!"

"John!" Teyla interrupted, putting her hand on his shoulder. "You have to calm yourself. Now is not the time to be putting the blame on anyone."

His jaw tightened, but he pulled his glare away from Rodney. Too many unknowns in this situation for his liking.

"Anyway," Rodney continued, his voice lower. "There's no good explanation for what happened. The other team was in there searching the place, touching the walls, the altar, making sure it was safe. No one else got zapped."

"So why Cooper?" Ronon asked, crossing his arms. Rodney could only offer a helpless shrug in response.

_"Colonel Sheppard, report to Dr. Weir's office. Colonel Sheppard."_

He passed a hand over his face, getting himself under control, then nodded. "Right. I gotta go, let me know if anything happens."


	4. Chapter 4

After his debriefing with Elizabeth, Sheppard didn't know what to do with himself. He couldn't go into the infirmary; they were still operating on Cooper. He couldn't eat, so going to the mess hall was useless. He tried spending time in his room, attempting to distract himself with magazines or _War and Peace_, but that didn't work, either.

People just kept dying. Granted, they were in a war, and people were going to die anyway no matter what happened. But even he, a soldier who'd seen so much death, couldn't get past it. Colonel Sumner getting the life sucked out of him. Lieutenant Ford, sent barreling down a path of self-destruction. Hell, he'd _watched_ Major Leonard blow himself to hell and could do nothing. And that was the heart of it. When it really came down to it, when it got to the point where someone died, it meant he could do nothing but stand by and watch. That was the problem with being so good at his job. It made the failures even harder to accept.

Shaking his head at his unwanted angst, Sheppard waved his door open, still not sure what he was going to do next. He didn't really have to decide. Ronon was standing there, as though just about to knock.

"Sorry," he grunted. "If you're busy-"

"Just busy torturing myself," Sheppard said gruffly. "I need something to do. Waiting around is killing me too slowly."

Ronon shrugged. "_Daedelus _just docked. We can help move supplies."

Best idea he'd heard all day. "Is that why you came over here?"

"I wanted to see if you were free."

Translation: _"I wanted to see if you were okay." _The Satedan was rarely anything but angry or unbothered, and wouldn't show it if he was. But after a time, the colonel had figured out Ronon's habits. He helped without letting someone know he was helping. He protected without making someone look weak. He changed what he could and didn't panic over the things he couldn't. A nice little island in a stormy sea.

Sheppard nodded, then they headed to the east dock. A few workers gave them curious looks and asked about what they were doing, but in the end nobody cared much what they did. The physical labor was good. It helped to clear Sheppard's mind of all those needling thoughts. Unfortunately, he couldn't do this forever, but he'd cross that bridge when he came to it.

"Colonel?"

He turned, seeing Colonel Caldwell standing a few feet behind him. "Sir."

"Have you been demoted?" he asked with slight amusement. "Wouldn't be a surprise after all the stunts you've pulled."

"No, sir, Ronon and I just figured we'd lend a hand. Show off for the lady dockworkers out here."

Caldwell nodded, then grew a little more serious. "What's the status, Colonel?"

Sheppard didn't even have to ask what he meant. "Not good, sir," he said quietly. "Last time I checked in, I was told there was some spinal damage. She might not... But we're hopeful."

The news seemed painful to the commander of the _Daedalus_, but he was a seasoned leader who wouldn't let it show. "Let's stay hopeful. She's a smart girl. And the timing couldn't be worse."

Sheppard's brow furrowed. "Sir?"

Caldwell looked up. "I'm bringing some news and some paperwork from the SGC. She was about to be promoted to Lieutenant Commander."

Lieutenant Commander. Right. Sometimes, it was easy to forget she'd originally come from the Navy. With that kind of rank, she could take control of a small ship if necessary. He remembered her fear of leading, how she second-guessed herself whenever she was in control, but he knew she'd be able to live up to the title. If she had the chance.

"I'll let her know when she wakes up, sir," he promised.


	5. Chapter 5

By the time everything calmed down in the infirmary, it was night and most of the people in Atlantis were asleep. Lorne was in the room, seated beside Cooper's bed and praying that she'd wake up. Of all the ways his paranoid mind imagined this mission going badly, this hadn't been one of them.

"Couldn't carry you out of there this time, MJ," he said quietly, holding her hand. "Sorry. I know you're pretty attached to that routine."

She didn't stir, and he hadn't really expected her to. Beckett said broken ribs, severe concussion, bruising almost everywhere, and damage to her spinal chord. It was generally assumed that she wasn't going to walk again, but that was if she woke up at all.

"I can't repair everything, much as I'd like to," the doctor had said. "It's up to her now, waking up. And with the state she's in... she might not want to."

Lorne disagreed. Cooper was tough, way tougher than she liked to give herself credit for. A lot of people liked to advertise when they'd stuck the landing in a bad situation, but she just kept going like it was business as usual. She had a sort of dry humor like Lorne's own that he found kind of charming. He didn't know what he'd do without dinners in the mess hall that started with, "So how was your day?" "Oh, you know. I'm being court martialed. Again."

His eyes wandered again to the heart monitor. Steady. Totally alive, except for the fact that she wouldn't wake up. In his experience, that was sort of the definition of dead, anyway.

"Major Lorne?"

He looked up. Teyla was standing there, holding a tray and looking surprised. "I'm sorry, I did not know anyone was in here."

He shook his head. "It's fine. Not like you were interrupting anything. Take a seat."

She pulled up a chair and sat down, letting her tray rest on the bed. He noticed a couple bowls, some candles, and a teapot there. "What's all this?"

She smiled slightly. "I came to send a prayer to the Ancestors for MJ's recovery. As it was within their own chamber that she was injured, I was hoping perhaps they might take some responsibility."

Lorne didn't believe in the power of the Ancients like the Athosians. Hell, sometimes he didn't believe much in his own god. It was selfish of him to suddenly turn to a heavenly being because he was in danger of losing someone important. But, nothing ventured, nothing gained. He might as well have a go.

"Alright. Tell me what to do."

Her smile widened and she began lighting the candles. "The art of prayer is much like that of meditation. It must be done with full concentration and devotion. You must not doubt yourself or those you ask for help."

He nodded, but a bit uncertainly. He of little faith wasn't about to devote his whole heart to something he didn't really believe in.

She then began to pour hot, flowery-smelling tea into one of the bowls. She mixed in a few of the herbs and whatnot that were on the tray, then held the bowl above her head. "We first give a toast to the Ancestors. An offering so that they may listen."

Really? Bribery? Then again, he'd witnessed several times how his own people offered help when they thought they'd get something in return.

Teyla looked at him, and something of his thoughts must have shown on his face because she said, "The aroma of the tea also helps for concentration, and to bring a more positive attitude to our minds."

They heard footsteps and looked to see Ronon and Sheppard pause on their way over, the latter looking slightly uncomfortable. "Ah, I just... came to check in. Caught Ronon lurking out in the hall, thought he'd better just come all the way in. We can go, if..."

"No, no," Teyla said quickly. "The more, the better. Come, join us."

They found two more chairs and pulled them up to the other side of the bed. Lorne noted how odd the scene was - Cooper down for the count, three men that didn't hold much stock in things they couldn't see, and Teyla, devoutly leading them in a traditional prayer. Not to mention the girly-ass tea fogging up his senses.

He wasn't trying to be difficult. She'd said he had to focus, and he was trying, but he believed in more tangible practices. What Dr. Beckett was doing, that was worth something. There was cold hard proof that his methods worked, and could work on Cooper. Lorne wasn't exactly sure what the Ancients were good for except getting them in a load of trouble.

"Ancestors," Teyla said aloud, her head bowed over the candles. "You built the life in this galaxy. You provided, you nurtured, and you preserved all that you could. We ask now for one more favor. We seek healing for our friend, for she was grievously injured in a place we believe you once inhabited, perhaps a holy place. She has served your galaxy without complaint in your absence. Bring her healing, bring her peace, and bring us beyond this long night."

She fell silent. After Ronon, Sheppard, and Lorne looked at one another, they closed their own eyes and attempted the level of concentration that Teyla was achieving.

He could have been imagining it - who knew what Teyla threw into that tea? - but for a moment, just for a second, he thought he felt a soft hand on his cheek.

_All will be well_, someone seemed to whisper, and then the feeling passed.

Teyla's hand slipped out of his, and then everyone seemed to stir. Sheppard was rubbing at his leg nervously, looking around. "No one... _heard_ anything, did they?" he asked.

Lorne wasn't sure why, but he wasn't too keen on telling everyone about the odd experience. He shook his head, as did Ronon. "Yeah, neither did I," said the colonel quickly.

Teyla smiled. "I did feel something. A... presence, perhaps. I believe our prayers will be answered."

A nice thought, but Lorne still had his doubts. He looked down at Cooper again, his thumb stroking her hand. "Sure hope so."


	6. Chapter 6

"Morning, John," Elizabeth said with a weary smile, watching as the colonel sat at her table for breakfast. "How are you feeling?"

He gave a half shrug. "Tired," he replied honestly.

She nodded. "Teyla told me about the prayer service you had last night. I'm sorry I missed it."

"It was kinda impromptu. I don't think any of us expected to get in on that." He poked at his food for a moment, looking consumed with his thoughts. Elizabeth wondered if she should prod, but it was sort of a fifty-fifty on what kind of answer she would get. He might avoid the question, he might tell her. It was better to not ask. He'd talk if he wanted to.

But after several minutes of uncomfortable silence, she finally had to break that rule. "John-"

"Do you believe in religion?" he asked suddenly.

She was taken aback by the question. "I believe any religion can have a certain amount of power, depending on the strength of faith of the believers."

"No, I mean, like, gods. Do you believe in God?"

She put her spoon down. "I try to keep an open mind. We've seen plenty of incredible things in our line of work. Why rule something like that out?"

"Well, because... I don't know, Rodney would argue that everything we've seen can be explained with science."

"Oh, I don't know. I still think there's an element of mystery to Ascension that will never go away." She let her chin rest on her hands, looking at him curiously. "You're not really the philosophical type, John. Why do you ask?"

He did that thing where he tilted his head back and forth, debating the best way to present his thoughts. She'd always found it a little amusing, seeing as everyone else on the expedition seemed so much more eloquent with their opinions. "Last night... might have been exhaustion, I don't know... or runaway hope, I guess. Rodney would laugh."

"What is it?"

He leaned forward. "Look, after Teyla said her prayer last night, I... felt something. I don't know what it was. But it was really... comforting. And I don't know about Lorne or Ronon, but Teyla said she felt it, too."

He was looking at her intently, as though she held the answers. And why shouldn't she? She was smart, logical, and normally had the answers for his questions. But not this time. "John, I can't tell you what you experienced," she said gently. "For all we know, it could have been the Ancients answering your prayers. Teyla has a very strong faith, and even on Earth, that's been known to move mountains."

He frowned. He wanted to not be confused about this, but it didn't look like that was going to happen.

"Dr. Weir, Colonel Sheppard."

They looked up, seeing Beckett standing by their table. Sheppard instantly tensed. "What? What's wrong?"

"Cooper's awake," he said, but his face said there was something more. "Everything's fine."

"You know, aside from the concussion and spinal damage," said the colonel.

Beckett shook his head. "No. I mean, _everything is fine_. She's perfectly alright, as though she never went into that chamber."

Elizabeth's eyes widened. "That's impossible."

"Try telling that to my machines."

They were both on their feet in an instant, not caring about the abandoned trays and following the doctor to the infirmary. Ronon, Rodney, Teyla, and Lorne were already there, standing around Cooper's bed.

"I swear, I feel fine," she said, a note of irritation in her voice. "Stop asking."

"You might want to give them a break, Cooper, this is a little hard to swallow," said Beckett. "In one night the diagnosis has gone from you possibly never walking again to being the picture of good health. It's definitely not something we see every day."

"I don't know, maybe your initial scans were wrong," she said, but even she knew that was a long shot. Beckett hardly ever made mistakes, especially not when operating on one of his friends.

"Do you think this might have something to do with whatever zapped her?" Sheppard asked.

"I thought about that," said Rodney. "That light looked an awful lot like what I got hit with a while ago, from that Ascension-o-Matic. Teyla said the chamber looked like a holy room, so who's to say that's not what that was?"

"You mean I'm going to Ascend?" Cooper asked.

"Maybe. Still not one-hundred percent sure, but when _I_ got hit with a funny light, I was able to heal people on the brink of death."

"It would make a bit of sense, at least," Beckett said. "When I first examined her, I found no evidence of any electrocution, though I believed what you said."

Teyla looked at them, then back at Cooper, shifting slightly. "I was thinking perhaps this was help of a different sort."

Ronon glanced down at her. "You mean the prayer?" He didn't say it doubtfully, nor did his tone say he didn't believe her. He respected Teyla, saw her as a sort of role model, was occasionally terrified of her, and genuinely wondered if she thought saying a few words and making funny-smelling tea had healed an entire person.

"I think it is not a coincidence that this happened so soon," she said. "And I remember feeling that presence last night, something that felt like assurance."

Sheppard shifted uncomfortably. He wondered if he should say something, but decided not to. Especially with Rodney getting that skeptical look.

"I understand your reasoning, Teyla," Elizabeth said. "There is the possibility that you're right."

"What, are you serious?" Rodney said, the smirk sliding off his face. "If saying a line of religious hooey actually worked, don't you think we'd use it a lot more often?"

"I'm not discounting it."

"Neither am I," said Ronon, to the surprise of everyone.

"Why not?" Cooper asked, who already had little enough clue as to what was going on.

The Satedan gave Beckett a meaningful look. "You told us about what happened during the stunner incident. You said the city was on Cooper's side." He gave a shrug. "I don't know about you, but it looks to me like the Ancestors have started picking favorites."

"Yes, but why?" Rodney countered. "Why should the Ancients give two shakes of a rat's ass what happens to her? It won't affect them at all, and the whole 'Ascension' thing means they've risen above those kinds of cares."

He shrugged. "Who knows? If they do care, why would they tell you about it?"

Rodney gaped for a moment like a fish out of water. He didn't like talking about his cosmic insignificance, especially if the caveman was the one bringing it up.

"Well, I, for one, am going to take whatever miracle I can get," Lorne said, patting Cooper's shoulder.

"All the same," Sheppard said. "We've learned sometimes it's better to look a gift horse in the mouth."

Elizabeth nodded. "I agree. I want to send your team back out to the planet to investigate that chamber. I know it's partially collapsed, but get as much as you can."

"We'll have to bring Cooper with us," Rodney said. "She's the one that can read the writing."

Elizabeth nodded, not looking happy about it. "I know. She'll have to go, too."

"I'm game," said the lieutenant, but Beckett held up a hand.

"I'd like to monitor her for at least another day, just to make sure there aren't any more surprises," he said.

Cooper nodded, if a bit reluctantly. "Fine. It's not like I can argue."

"You won't be lonely, Coop. Somebody will be in here with you," Sheppard said, patting her foot.

"Yes, and that's another thing. If we could cut down on the amount of people in here, I think that would be easier on everyone," Beckett added.

"Right. I have to get back to the lab, anyway," said Rodney. "Cooper, um... glad to see you're okay."

Sheppard and Ronon also took their leave, then Teyla, after touching her forehead to Cooper's. Beckett excused himself after checking the monitor one more time. Then it was only Elizabeth and Lorne.

Cooper frowned, shaking her head slightly. "I spend way too much time in here."

Elizabeth smiled. "But you never stay for long."

"Yeah, but in all the times I've seen you bounce back, it hasn't been this good," Lorne said.

"And you're _sure_ you're okay?" Elizabeth pressed. "You feel like yourself? No strange urges?"

She shook her head. "No. As far as I know, I'm me."

Elizabeth held her gaze for a moment. She knew, from personal experience, that if the lieutenant did feel out of sorts, she might not give voice to it. But Cooper seemed genuinely okay - as Beckett said, like she had never even been in that chamber.

"Alright. Let me know if anything does start feeling different. Lorne, I want you keeping an eye on her, too."

"Yes, ma'am," said the major, giving a respectful nod as she left.

She paused. "Oh, and Major?"

"Yes, Doctor?"

She had a glint of amusement in her eyes. "Try to keep the PDA to a minimum. There are certain astrophysicists who find your relationship uncomfortable."

He looked down, trying to hide his grin. "I'll do my best, Doctor."

Cooper watched Elizabeth leave, then looked up at Lorne, curling her hand around his. "You didn't stay here all night, did you?"

He gave a small smile, seating himself in the chair. "What tipped you off?"

"Oh, you just look sixty years old instead of thirty-two."

"Oh, really?" he chuckled. Then his smile grew slightly more tender and he lifted her hand to his lips, kissing the soft skin.

"Careful," she said quietly, as though to whisper something sweet to him. He leaned closer. "Kavanagh might be lurking around the corner."

He laughed. "Then I might as well give him that show, huh?" he murmured, leaning forward and kissing her. "Please stop trying to kill yourself, Cooper."

"Hey, Pegasus is trying to kill me-"

He cut her off with another kiss. "Just say 'okay' and we'll call it good."

She looked into his eyes, for the moment, feeling drowsy, comfortable, and, for the moment, happy. "Okay."


	7. Chapter 7

The next day, Cooper and Sheppard were standing on the balcony overlooking the city. He was feeling a little less stressed, now that she was willingly sharing his company. But there was still tension in the air due to the fact that neither person had much of a clue as to what had happened.

"I feel really weird about this, sir," she said, shaking her head at the horizon.

"Yeah, you and me both," he agreed. "But, hey, at least you don't have a panic attack every time I walk into the room."

She grimaced. "I feel... at ease now. And that makes me uncomfortable."

He looked at her, trying not to feel sorry for her because he knew she wouldn't want his pity. She wanted answers, not apologies. "Soon enough, we'll head back to the chamber. Then you can investigate to your little heart's content."

She nodded, continuing to look out over the water. She leaned further against the railing, looking down at the lower parts of the city. He frowned. Ever since she'd gotten out of the infirmary, she'd been taking everything in like a tourist, even though she'd been living there for months. "Are you okay?"

"It's like I'm looking at everything with new eyes. I remember every inch of this place, but..." She shook her head. "At the same time, it's like I've never seen it before."

"You took a pretty hard knock on the head. Miracle healing or not, that's bound to make you go a little looney."

"I'm not looney."

"Acceptance is the first step to getting help."

"I'm not-" She shook her head. "I just want to feel normal."

He patted her back. "You're normal, Cooper. It's everyone else that's crazy."

**. . .**

Back on the desert planet, and there was a distinct uneasiness about the team. Rodney stayed back on Atlantis, probably still fearing for the structural integrity of the chamber, but Lorne's squad had accompanied them in the event of any more accidents. Cooper had to admit, having the major there made her heart beat a little more steadily than it might have.

But she was still scared, if only a bit. She wore her calm demeanor like armor on the outside, but inside she was burning with questions and doubts. Something about that chamber wasn't right at all.

They stopped around the rectangular hole. Several scientists were already at the site, examining the stone a few feet away that had triggered it all. None of the scientists were down in the hole, whether because they hadn't gotten to it yet or because they were afraid, she didn't know.

_I should be dead_, she thought. _Or at least close to it_. She could see where the wall had collapsed from here as she crouched at the ledge. There was a lot of heavy rock.

"You don't have to go down there," Lorne reminded her gently.

"I would gladly go first if you so wish," Teyla said.

Cooper took a deep breath, thinking of what she'd been through and how much she still didn't know. "No, that's okay." Shoving her fears aside, she seized hold of the cables and dropped down into the hole.

Her boots hit the dirt and she moved a few paces forward. Seconds later there was the sound of polyester rubbing on nylon and Teyla, Sheppard, and Lorne joined her in the small space.

"Notice anything?" Sheppard asked, looking around even as he kept an eye on her.

She _did_ notice something. She just wasn't ready to voice it. As she examined the chamber, the writing on the walls shifted. Sometimes, she thought she could understand what was there as plain as English, and then she would look harder and it would go back to being gibberish. It started making her dizzy, and a headache rapidly began making her lose concentration.

"Cooper," Sheppard said carefully. "You okay?"

"Fine, sir," she said, but her voice was quiet. Her head was pounding, and she had to stay still or the shifting writing would make her fall over.

"Cooper." He took her shoulder and turned her to face him, frowning at what he saw. "Cooper, nosebleed."

"What?" She recovered from the turn and touched a finger to her face. Blood.

"I think that's enough," Lorne said. "We should go."

"I haven't done anything-"

"We're going," Sheppard agreed firmly.

"You are unwell, MJ," Teyla said. "Perhaps it was not wise to bring you here."

"I'm fine," Cooper insisted, but they weren't listening.

"I'd rather not risk it," Lorne said as he pushed her gently towards the cables. They sent her up first, as though unsure if she'd be able to make it all the way by herself. She was capable, of course, but the pounding and dizziness in her head was slow to wear off. When the others hauled themselves out, they found her lying on the ground.

"You okay?" Sheppard asked, trying to sound nonchalant.

"I have to wait for the ground to stop spinning."

He nodded. "Right. Well, when you get your feet back, we're out of here."

"Don't make any plans just yet," Ronan said, and they all heard him audibly preparing his weapon.

"Sir!" cried one of the soldiers stationed near the Stargate. "Sir! Offworld activation!"

As though they couldn't clearly see it. The wormhole plunged into the world, then the soldiers gave the shimmering ring a wide berth. As everyone watched, the nose of a Wraith Dart began to emerge.

"You up for a fight, Cooper?" Sheppard said tensely.

"Always, sir," she grunted, heaving herself to her feet.


	8. Chapter 8

**Sorry for the delay, I've been at band camp. Updates will resume.**

**. . .**

The Marines nearest the Gate were hit hard, but they were put on the Atlantis expedition for a reason. When the Wraith Darts came through, guns blazing, the men ducked for cover and fired whenever they had the chance. The scientists studying the flat stone were lowered into the chamber, as there was no other suitable cover. And that was precisely the problem.

"There's nothing to cull here, what are they doing?" Lorne asked, crouched behind a mound of sand.

"Maybe they knew we were here. The chamber _did_ belong to the Ancients, maybe they know what it does," Sheppard said. "And, you know, any excuse to take us out is fine by them."

Cooper had taken cover with Teyla and Ronon some several yards away behind a larger sand dune. The Wraith had only sent Darts, but there were several of them. Ronon took aim at one passing by, his gun set to the maximum setting. Most of one wing was blown off, sending the ship spinning off to the ground.

"Can you hold up?" he asked, looking at Cooper intently.

She nodded. "I'm fine."

"Your nose is still bleeding a little."

"It's a nosebleed, not a brain hemorrhage." She opened fire on the next Dart, but didn't get very far.

"Wait, look there!" Teyla said, craning her neck as far as she dared over the sand. Ronon and Cooper followed her gaze, looking towards the underground chamber. Four Wraith were approaching the opening, being cautious about every step.

"They want whatever's in the chamber," Cooper said.

"Yeah, and they're not gonna get it," Ronon said.

"Well, do we want to run out in full view of the Darts, or sacrifice our aim to stay hidden?" Cooper asked.

You two and Lorne should go fight them head-on," Ronon said. "Sheppard and I can handle the Darts." He leaned closer to his radio. "How about it, Sheppard?"

"_Copy that. Lorne, Cooper, and Teyla, move in before they start shooting the scientists."_

"Understood," Cooper said. She and Teyla moved out from cover on the balls of their feet. Once they were out in the open, they sprinted across the sand to the Wraith. From the corner of her eye, Cooper saw Lorne doing the same. Several missiles from a Dart landed near them, waves of heat billowing over the soldiers, but in a moment they could hear the ship making a rough descent. Cooper stood with flexible posture, tensed and ready to move at a moment's notice, then fired on one of the Wraith. He fired back and she dodged, rolling a few feet away. Always stay moving. That's how you survive a gunfight.

As her Wraith went down, so did Teyla's, but she noticed a few more advancing on the site. Three of Lorne's men had joined the team, but Cooper had the feeling that it wouldn't be enough. It usually took at least two soldiers to bring a Wraith down for good, and after bringing one down she was running out of ammo.

Dust was flying everywhere, kicked up by the gunfire and the many feet. She wondered if maybe so many people up here would be a problem for the chamber below, but there wasn't much she could do about it.

"Cooper, look out!" Lorne shouted above the din. She wasn't quick enough to turn. A Wraith seized her from behind, his cold fingers digging into the soft flesh of her neck. She pointed her P-90 behind her and squeezed the trigger. He let go, but was by no means incapacitated.

She turned and pulled the trigger again, but only got two shots off before the bullets stopped coming. No time to reload. She raised the butt of the gun and slammed it into the Wraith's head, but he was so much stronger than that. It was barely more than a slap to him. His fist caught her jaw and she sprawled on the ground, marveling at the power in one limb. Her senses returning, she aimed a hard kick at his legs, hitting the back of the knee and throwing him off balance. But before she could scramble to her feet, he let himself fall, all of his weight going to one knee as he landed on her lower ribs. All the air rushed out of her and the continued weight made it hard to retrieve.

She felt the cold end of a Wraith weapon at her chin. An explosion not too far away caused the ground to shudder and a cloud of dust to billow over Cooper and her adversaries. No one could see them. No help would come.

Then, not so much an idea as an instinct overwhelmed her. She reached up, her hand grasping at the Wraith's throat.

Then she was blinking, feeling like she was opening her eyes after holding them closed, and saw the dead Wraith, her hand still resting on his collar. There was a part of her that felt a little empty, like a huge amount of energy had just been exerted, but she couldn't understand how.

She scrambled backward, confused and a little horrified at what had just happened. She stared at her hand, which was shaking like a hula girl an a trucker's dashboard. _What the hell…?_

Before she could investigate any further, strong hands gripped her shoulders and pulled her to her feet. "Cooper, you okay?" Lorne asked, turning her to face him.

She couldn't answer for a moment. He was still holding on to her, and she was using that to remain standing, because her legs were shaking too much for her to do it on her own.

"Cooper, can you hear me?"

"I can hear you," she said. "I'm - I'm not hurt, I'm okay."

He looked like he didn't believe her, but he decided the questions could wait. "Fight's over. The colonel has a live one under his boot, let's see what he has to say."

She nodded and turned to begin walking, but Lorne wordlessly took her arm and turned her in the right direction. She was breathing a little easier now, not panicking so much, but the shaking wasn't going away.

"You just hurt a lot of people, buddy, how about you explain yourself?" Sheppard was saying to the Wraith pinned firmly to the ground by his boot and several rifles. "What are you doing here?"

"Trying to rid the thorn in our side," the Wraith said.

"_Why_ are you _here_?" The pressure of Sheppard's foot increased and the Wraith groaned slightly.

"You were not careful," he said. "The chamber has been under watch for months. You opened the door for us."

"Yeah, and you got your asses kicked."

"It is inconsequential. More will come."

Sheppard looked around at his teams, but everyone looked as nonplussed as he did. "Why? What's so important about this chamber?" When the Wraith remained quiet, he pressed harder again. "I said, what's so important about-"

"If I knew, I would not tell you."

He sighed, then slammed the butt of his gun as hard as he could against the Wraith's head, knocking him out cold. Sheppard was definitely better at that than Cooper. "Alright, let's pack up and get out of here."

"All the equipment, too, sir?" Lorne asked.

"Yeah. We're not coming back, not for exploration. You heard what he said, checking this place out is a danger I don't want to risk right now." He stepped away from the Wraith and made the sign to move out.

"We still do not know why they wanted the chamber in the first place," Teyla said.

"Right, and we're not gonna find out by waiting for the next wave to ask." He glanced at Cooper, and she didn't miss the hurriedly hidden uneasiness in his eyes. "Something is _not_ right about that room. We need to proceed with a lot more caution."

She ran a hand across the bruise blossoming on her collarbone. Sheppard walked away, but she could still feel that distrustful look. She'd finally stopped being nervous around him, and now he was afraid of her. And, as she passed the Wraith she'd killed, she really couldn't blame him.


	9. Chapter 9

Cooper tried to focus on the soothing hum of Atlantis, the slight vibration that was a telltale sign of the city's life. She was breathing deeply, easing the rate of her heart. But there was no forgetting, no ignoring what happened. Lieutenant Cooper had killed a Wraith with her bare hand and had no idea how.

She didn't want to tell anyone because then she'd be put in isolation, under watch, and it would solidify the fact that something was very wrong with her. Maybe it was a fluke, a combination of events that caused the Wraith to die in such a spectacular way. It might never happen again.

Or maybe it would. And maybe to someone who wasn't an enemy.

It was a moment before she realized her door was chirping at her. "Come in," she said quickly, wondering how many rings she'd missed.

Lorne entered, giving her a small smile. "Hey."

She smiled weakly back. "Hi."

She felt a bit more comfort when he sat beside her on the bed, his leg touching hers. "How are you doing?"

"Uh…." She ran a hand through her hair. "Okay, I guess."

"You've been pretty jumpy since the last mission. Is this still about Sheppard, or is it… the other thing?" he asked.

That's what he'd been calling it. "The other thing," because it had no name, no particular category. "No, Sheppard doesn't scare me. It's… I don't know, it's a lot of things. I want to know what happened to me and why the Wraith seemed to want the chamber so badly."

"Teyla did say it might be some kind of healing chamber," he offered. "Anybody would want that, especially if it heals wounds as bad as yours were."

She took a breath, letting Lorne's rationality wash over her. "Thank you. I needed that."

He grinned a little. "What?"

"Somebody with some sense. I'm losing my mind a little bit here." She leaned against him, smiling slightly. "How are _you_, Major Lorne?"

"Well, I feel a little better now that you're smiling again." He leaned over and kissed her softly. "How about some lunch?"

"That sounds fine," she said. She let him go first, collecting herself. She was now desperately ignoring the fact that, as he'd kissed her, there was just a tiny piece in the back of her mind that kept saying, _I don't want this_.

**. . .**

Elizabeth Weir sat in her office finishing a few reports, and signing off on the ones Sheppard had just dropped off. It was late, too late by normal standards, but Elizabeth was a steadfast worker and scientist. If there was knowledge within reach, she could sleep when she was dead.

Then the door opened without announcement. She looked up, then straightened in surprise. "Lieutenant Cooper. Shouldn't you be asleep-"

"I apologize for the abruptness of my arrival, but I needed to speak with you immediately," said Cooper, but she didn't sound quite like Cooper. She had gained an accent, and a grave composure.

"Lieutenant, what's going on?" Elizabeth asked warily.

"At the moment, you are not speaking with Mary Jane Cooper," she said. She blinked, and when her eyes opened again, they glowed like tiny stars.

Elizabeth stood, her hand already going to her radio. "What the hell are you?"

"Be still, Dr. Weir, I mean you no harm," said the being, raising a passive hand. "My name is Ayallah. I am not here as an enemy, but as a potential ally."

"Then why are you inside one of my team members?" Elizabeth demanded. "You've stolen a body. Does she even know you're in there?"

"No, she does not," said Ayallah, and her eyes dimmed slightly in an almost sad way. "And that is the way I wish it to remain. I needed to take a body because I was dying. My Ascension was never complete and I hid myself in a chamber until a proper host could be found."

The doctor cocked her head. "Ascension? Are you - Do you mean to tell me that you're one of the Ancients?"

"Yes, that is how your people refer to us."

"But why Cooper? At least three other people entered that chamber, why did you choose her?"

Ayallah reached up and pulled at the sleeve of her shirt, exposing the tattoo on Cooper's left arm. "She bore the mark of the chosen."

Elizabeth's eyes widened. Oh, how horribly wrong this could go. "That's a _tattoo_, Ayallah. Cooper got it when she was eighteen, it's not a 'chosen mark.' It's a delta."

Ayallah's brow furrowed. "If she was not a decent host, her mind would have burnt as I entered. But, as your doctor has determined, Mary Jane is absolutely fine."

"Yeah, more than fine, from what I've heard." She put her hands on the back of her chair, trying to control her anger. "What are you doing to her? And shouldn't you ask permission for something like this?"

"I assure you, this sort of case is exceedingly rare. And, as I said, she bore the mark. I had thought that was permission enough. I will ask you to not worry, as the only effect I am having is to make her as well as possible."

"But she _didn't_ give you permission. You know that now, is there any way to leave her body?"

Ayallah frowned. "I told you before, Dr. Weir, I was dying. It took a long time for a host to enter my chamber. I would be too weak to survive now outside of Mary Jane's body, and even if I wanted to, I would be unable to step out."

"Why not?"

"Because I never fully Ascended. I am a mass of uncontrolled energy out in the world and I could do great damage to the city's mainframe."

Elizabeth frowned, then looked back at Sheppard's report. "That explains Rodney's energy readings."

"Indeed." Ayallah clasped her hands, looking at the doctor imploringly. "My staying here will benefit both of us, I promise. I can use my powers to help you on your missions, and in return I am allowed to survive."

"But you don't want anyone to know of this?" Elizabeth said.

She shook her head. "No. If I am to assimilate, I will have no one treating me differently. Perhaps, in time, I will inform the others. For now, it is easier to earn their trust this way. I inform you because you are the leader and it is your right to know."

"It's _her_ body! Don't you think she has a right to know?" she snapped.

"I cannot trust her to keep this a secret. She is my host, but I cannot control her thoughts or influence her actions. I can only emerge when I wish."

The doctor sighed. "Well, at least there's that." She shook her head. In all her time in Atlantis, she'd rarely felt so backed against a wall. "You're not giving me much choice here. Whether I like it or not, I suppose you'll have to stay."

Ayallah nodded respectfully, then slowly raised her head. "There is one other option. If you decide at some point that you cannot abide me here, that I am fully unwelcome, then there is the possibility of you having me discharge on another planet, where I will not harm anyone."

"But eventually die?"

She nodded again. "Yes."

Elizabeth sighed. Her anger was fizzling out when the death of another came into the equation, especially the death of an Ancient. "No. If you're as helpful as you say, I don't think it'll come to that. But rest assured, Ayallah, if I decide my team needs to know about this, I _will_ tell them."

"Agreed." Ayallah gave one last respectful bow, then turned to leave the room.

"Wait, one more question." Elizabeth waited until she turned to continue. "This discussion... will Cooper remember any of it?"

Ayallah shook her head. "No. My mind is present at this time, and it is with my mind that you have been conversing. She will not remember any times when I emerge."

Elizabeth nodded. "Right. Go back to her room. And please, don't wander the halls like this anymore."

"Thank you, doctor."

Elizabeth watched her go, entirely unhappy with the turn of events, but willing to make the best of it if she had to. Atlantis had always depended on that.


End file.
